aaalgo/lung_example

PythonBSD-2-Clause

lung_example

Prerequisites:

SimpleITK (for Luna16): http://www.simpleitk.org/SimpleITK/resources/software.html
git clone https://github.com/aaalgo/aardvark so that aardvark and lung_example are in parallel.

Tasks to do:

Setup C++ code. (./setup.py build)
Setup Luna16 data. Create symbolic link so that theres lung_example/luna16 which contains the following content.

luna16/
├── CSVFILES
│   ├── annotations.csv
│   ├── candidates.csv
│   └── sampleSubmission.csv
├── subset0
│   ├──
1.3.6.1.4.1.14519.5.2.1.6279.6001.105756658031515062000744821260.mhd
│   ├──
1.3.6.1.4.1.14519.5.2.1.6279.6001.105756658031515062000744821260.raw

Setup scratch directory under lung_examle. It could be a simbolic link to some storage with at least 250G space.
Run ./import_lung.py to preprocess Luna16 data.
Run ./visualize_nodules.py to generate some sample visualization.
Run ./train.py to start training. No need to finish. Kill it after the progress bar starts moving.